\documentclass[a4paper]{book}
\usepackage{makeidx}
\usepackage{graphicx}
\usepackage{multicol}
\usepackage{float}
\usepackage{listings}
\usepackage{color}
\usepackage{ifthen}
\usepackage[table]{xcolor}
\usepackage{textcomp}
\usepackage{alltt}
\usepackage{ifpdf}
\ifpdf
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\usepackage[utf8]{inputenc}
\usepackage{mathptmx}
\usepackage[scaled=.90]{helvet}
\usepackage{courier}
\usepackage{sectsty}
\usepackage[titles]{tocloft}
\usepackage{doxygen}
\lstset{language=C++,inputencoding=utf8,basicstyle=\footnotesize,breaklines=true,breakatwhitespace=true,tabsize=8,numbers=left }
\makeindex
\setcounter{tocdepth}{3}
\renewcommand{\footrulewidth}{0.4pt}
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\begin{document}
\hypersetup{pageanchor=false}
\begin{titlepage}
\vspace*{7cm}
\begin{center}
{\Large turboOrtho \\[1ex]\large 0.9.7.6 }\\
\vspace*{1cm}
{\large Generated by Doxygen 1.7.4}\\
\vspace*{0.5cm}
{\small Sat Dec 31 2011 17:51:08}\\
\end{center}
\end{titlepage}
\clearemptydoublepage
\pagenumbering{roman}
\tableofcontents
\clearemptydoublepage
\pagenumbering{arabic}
\hypersetup{pageanchor=true}
\chapter{Todo List}
\label{todo}
\hypertarget{todo}{}
\input{todo}
\chapter{Module Index}
\input{modules}
\chapter{Class Index}
\input{annotated}
\chapter{File Index}
\input{files}
\chapter{Module Documentation}
\input{group__filtering}
\input{group__pipe__filters}
\input{group__filter__container}
\input{group__filter__transport__container}
\input{group__filtering__ops}
\chapter{Class Documentation}
\input{classblast__filtering}
\input{structbucket__norm}
\input{structbucket__pipe__binary}
\input{classbuild__string}
\input{classpipe__binary}
\input{classpipe__bucket}
\input{classpipe__merge}
\input{classpipe__norm}
\input{classpipe__struct}
\input{classpipe__write}
\input{classtaxon__pair}
\chapter{File Documentation}
\input{blast__filtering_8h}
\input{blast__filtering__main_8h}
\input{bucket__norm_8h}
\input{bucket__pipe__binary_8h}
\input{build__string_8h}
\input{enum__write__list__t_8h}
\input{pipe__binary_8h}
\input{pipe__bucket_8h}
\input{pipe__merge_8h}
\input{pipe__norm_8h}
\input{pipe__struct_8h}
\input{pipe__write_8h}
\input{taxon__pair_8h}
\printindex
\end{document}
